FMO DATABASE

FMODB ID: ZZ6MN

Calculation Name: 1WDC-C-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1WDC

Chain ID: C

ChEMBL ID:

UniProt ID: P07291

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	152
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1334565.399331
FMO2-HF: Nuclear repulsion	1273487.87633
FMO2-HF: Total energy	-61077.523001
FMO2-MP2: Total energy	-61252.746962

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)

Summations of interaction energy for fragment #1(A:3:LEU)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-439.946	-426.678	12.93	-8.608	-17.589	-0.077

Interaction energy analysis for fragmet #1(A:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.830 / q_NPA : 0.910

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	5	GLN	0	-0.072	-0.039	3.779	-4.820	-3.194	-0.001	-0.924	-0.700	0.001
5	A	7	GLU	-1	-0.848	-0.930	2.815	-59.193	-57.054	0.259	-0.871	-1.528	-0.007
6	A	8	ILE	0	-0.067	-0.029	2.243	-0.106	0.958	2.549	-0.654	-2.958	-0.002
7	A	9	ASP	-1	-0.857	-0.920	4.209	-24.271	-24.097	0.001	-0.037	-0.138	0.000
9	A	11	LEU	0	-0.029	-0.012	3.286	2.009	2.350	0.016	-0.064	-0.293	0.000
67	A	69	LEU	0	-0.040	0.002	2.514	-2.240	-2.165	1.211	-0.163	-1.123	0.000
68	A	70	PRO	0	-0.006	-0.005	3.668	-5.280	-4.783	0.015	-0.158	-0.354	-0.001
70	A	72	TYR	0	0.057	0.008	2.269	0.440	1.254	2.730	-0.838	-2.707	-0.010
71	A	73	GLU	-1	-0.948	-0.985	2.268	-88.846	-82.567	3.853	-4.451	-5.680	-0.052
72	A	74	GLY	0	-0.023	-0.012	3.456	0.788	0.891	0.033	0.078	-0.214	-0.001
74	A	76	MET	0	-0.026	-0.005	3.080	-1.851	-1.695	2.264	-0.526	-1.894	-0.005
4	A	6	ASP	-1	-0.893	-0.950	5.960	-29.841	-29.841	0.000	0.000	0.000	0.000
8	A	10	ASP	-1	-0.844	-0.924	6.795	-26.103	-26.103	0.000	0.000	0.000	0.000
10	A	12	LYS	1	0.803	0.900	6.507	30.080	30.080	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.896	-0.938	9.312	-18.463	-18.463	0.000	0.000	0.000	0.000
12	A	14	VAL	0	-0.038	-0.024	9.449	1.765	1.765	0.000	0.000	0.000	0.000
13	A	15	PHE	0	-0.033	-0.010	9.410	1.118	1.118	0.000	0.000	0.000	0.000
14	A	16	GLU	-1	-0.924	-0.976	11.299	-14.994	-14.994	0.000	0.000	0.000	0.000
15	A	17	LEU	0	-0.081	-0.030	14.188	1.245	1.245	0.000	0.000	0.000	0.000
16	A	18	PHE	0	-0.009	-0.029	13.827	1.015	1.015	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.720	-0.854	15.288	-13.783	-13.783	0.000	0.000	0.000	0.000
18	A	20	PHE	0	-0.116	-0.058	16.992	1.079	1.079	0.000	0.000	0.000	0.000
19	A	21	TRP	0	-0.091	-0.055	19.080	1.135	1.135	0.000	0.000	0.000	0.000
20	A	22	ASP	-1	-0.867	-0.932	18.344	-13.722	-13.722	0.000	0.000	0.000	0.000
21	A	23	GLY	0	-0.054	-0.019	20.891	0.512	0.512	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.889	0.949	19.451	13.146	13.146	0.000	0.000	0.000	0.000
23	A	25	ASP	-1	-0.971	-0.985	19.714	-12.504	-12.504	0.000	0.000	0.000	0.000
24	A	26	GLY	0	-0.039	-0.015	16.542	0.017	0.017	0.000	0.000	0.000	0.000
25	A	27	ALA	0	-0.074	-0.047	15.392	-0.996	-0.996	0.000	0.000	0.000	0.000
26	A	28	VAL	0	0.037	0.049	13.339	0.553	0.553	0.000	0.000	0.000	0.000
27	A	29	ASP	-1	-0.779	-0.902	15.425	-13.474	-13.474	0.000	0.000	0.000	0.000
28	A	30	ALA	0	0.009	-0.017	14.941	-0.774	-0.774	0.000	0.000	0.000	0.000
29	A	31	PHE	0	-0.092	-0.047	15.966	-0.296	-0.296	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.871	0.921	15.463	13.827	13.827	0.000	0.000	0.000	0.000
31	A	33	LEU	0	0.021	0.027	9.624	-0.576	-0.576	0.000	0.000	0.000	0.000
32	A	34	GLY	0	0.042	0.012	11.219	-1.345	-1.345	0.000	0.000	0.000	0.000
33	A	35	ASP	-1	-0.857	-0.928	12.647	-15.544	-15.544	0.000	0.000	0.000	0.000
34	A	36	VAL	0	0.016	0.013	8.581	-0.254	-0.254	0.000	0.000	0.000	0.000
35	A	37	CYS	0	-0.016	-0.012	8.084	-1.860	-1.860	0.000	0.000	0.000	0.000
36	A	38	ARG	1	0.853	0.924	8.982	15.848	15.848	0.000	0.000	0.000	0.000
37	A	39	CYS	0	-0.105	-0.048	11.619	0.813	0.813	0.000	0.000	0.000	0.000
38	A	40	LEU	0	-0.024	-0.003	5.282	0.297	0.297	0.000	0.000	0.000	0.000
39	A	41	GLY	0	-0.017	0.001	8.127	-1.515	-1.515	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.015	0.018	6.705	0.663	0.663	0.000	0.000	0.000	0.000
41	A	43	ASN	0	-0.082	-0.068	10.022	1.248	1.248	0.000	0.000	0.000	0.000
42	A	44	PRO	0	0.040	0.027	11.004	0.831	0.831	0.000	0.000	0.000	0.000
43	A	45	ARG	1	0.858	0.916	13.490	16.256	16.256	0.000	0.000	0.000	0.000
44	A	46	ASN	0	-0.009	-0.029	15.930	-1.209	-1.209	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.918	-0.948	17.863	-14.452	-14.452	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.817	-0.905	13.204	-18.501	-18.501	0.000	0.000	0.000	0.000
47	A	49	VAL	0	0.006	-0.003	12.788	-0.769	-0.769	0.000	0.000	0.000	0.000
48	A	50	PHE	0	-0.044	-0.030	14.287	0.336	0.336	0.000	0.000	0.000	0.000
49	A	51	ALA	0	-0.036	-0.001	14.958	0.275	0.275	0.000	0.000	0.000	0.000
50	A	52	VAL	0	-0.023	0.001	9.698	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	53	GLY	0	-0.022	-0.005	12.671	-0.264	-0.264	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.041	0.027	15.099	0.274	0.274	0.000	0.000	0.000	0.000
53	A	55	THR	0	-0.081	-0.042	15.980	0.478	0.478	0.000	0.000	0.000	0.000
54	A	56	HIS	1	0.855	0.917	19.598	12.646	12.646	0.000	0.000	0.000	0.000
55	A	57	LYS	1	0.888	0.951	22.644	10.707	10.707	0.000	0.000	0.000	0.000
56	A	58	MET	0	0.046	0.043	20.623	-0.454	-0.454	0.000	0.000	0.000	0.000
57	A	59	GLY	0	-0.061	-0.041	22.349	0.543	0.543	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.926	-0.965	22.072	-11.448	-11.448	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.881	0.924	15.734	16.303	16.303	0.000	0.000	0.000	0.000
60	A	62	SER	0	0.019	0.031	17.342	-0.031	-0.031	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.038	-0.018	12.511	0.328	0.328	0.000	0.000	0.000	0.000
62	A	64	PRO	0	0.075	0.049	13.141	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	65	PHE	0	0.033	0.010	6.063	-1.098	-1.098	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.923	-0.983	8.113	-22.319	-22.319	0.000	0.000	0.000	0.000
65	A	67	GLU	-1	-0.969	-0.992	8.793	-18.902	-18.902	0.000	0.000	0.000	0.000
66	A	68	PHE	0	0.020	-0.004	7.552	-0.852	-0.852	0.000	0.000	0.000	0.000
69	A	71	ALA	0	-0.004	0.004	5.617	-0.196	-0.196	0.000	0.000	0.000	0.000
73	A	75	LEU	0	-0.018	-0.019	7.041	2.784	2.784	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.964	-0.968	6.167	-34.702	-34.702	0.000	0.000	0.000	0.000
76	A	78	CYS	0	-0.094	-0.027	8.934	2.914	2.914	0.000	0.000	0.000	0.000
77	A	79	GLU	-1	-0.948	-0.983	11.690	-15.435	-15.435	0.000	0.000	0.000	0.000
78	A	80	GLN	0	0.025	0.017	11.760	-0.286	-0.286	0.000	0.000	0.000	0.000
79	A	81	GLY	0	0.015	0.018	15.827	0.220	0.220	0.000	0.000	0.000	0.000
80	A	82	THR	0	-0.042	-0.066	19.231	-0.060	-0.060	0.000	0.000	0.000	0.000
81	A	83	PHE	0	0.028	-0.007	21.195	0.511	0.511	0.000	0.000	0.000	0.000
82	A	84	ALA	0	-0.045	-0.017	24.100	0.517	0.517	0.000	0.000	0.000	0.000
83	A	85	ASP	-1	-0.755	-0.847	22.453	-12.645	-12.645	0.000	0.000	0.000	0.000
84	A	86	TYR	0	0.000	-0.007	19.223	0.627	0.627	0.000	0.000	0.000	0.000
85	A	87	MET	0	-0.049	-0.006	26.110	0.504	0.504	0.000	0.000	0.000	0.000
86	A	88	GLU	-1	-1.011	-1.001	28.887	-9.786	-9.786	0.000	0.000	0.000	0.000
87	A	89	ALA	0	0.032	0.013	27.996	0.350	0.350	0.000	0.000	0.000	0.000
88	A	90	PHE	0	0.035	0.011	27.361	0.370	0.370	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.936	0.980	31.876	9.085	9.085	0.000	0.000	0.000	0.000
90	A	92	THR	0	-0.101	-0.058	33.286	0.323	0.323	0.000	0.000	0.000	0.000
91	A	93	PHE	0	0.002	0.000	32.127	0.224	0.224	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.788	-0.864	36.672	-7.750	-7.750	0.000	0.000	0.000	0.000
93	A	95	ARG	1	0.904	0.942	38.392	7.189	7.189	0.000	0.000	0.000	0.000
94	A	96	GLU	-1	-0.928	-0.958	41.943	-6.669	-6.669	0.000	0.000	0.000	0.000
95	A	97	GLY	0	-0.042	-0.003	40.477	0.102	0.102	0.000	0.000	0.000	0.000
96	A	98	GLN	0	-0.087	-0.047	40.820	0.054	0.054	0.000	0.000	0.000	0.000
97	A	99	GLY	0	-0.016	-0.014	36.493	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	100	PHE	0	-0.007	-0.022	36.323	-0.127	-0.127	0.000	0.000	0.000	0.000
99	A	101	ILE	0	0.024	0.015	33.723	-0.014	-0.014	0.000	0.000	0.000	0.000
100	A	102	SER	0	0.067	0.031	37.178	-0.047	-0.047	0.000	0.000	0.000	0.000
101	A	103	GLY	0	0.065	0.033	36.073	-0.215	-0.215	0.000	0.000	0.000	0.000
102	A	104	ALA	0	-0.045	-0.027	36.037	-0.147	-0.147	0.000	0.000	0.000	0.000
103	A	105	GLU	-1	-0.928	-0.976	36.410	-8.217	-8.217	0.000	0.000	0.000	0.000
104	A	106	LEU	0	-0.005	0.007	29.932	-0.186	-0.186	0.000	0.000	0.000	0.000
105	A	107	ARG	1	0.815	0.874	31.924	8.357	8.357	0.000	0.000	0.000	0.000
106	A	108	HIS	0	0.000	0.018	32.950	-0.166	-0.166	0.000	0.000	0.000	0.000
107	A	109	VAL	0	0.001	-0.012	30.357	-0.184	-0.184	0.000	0.000	0.000	0.000
108	A	110	LEU	0	-0.006	0.003	26.538	-0.278	-0.278	0.000	0.000	0.000	0.000
109	A	111	THR	0	0.012	0.013	28.384	-0.189	-0.189	0.000	0.000	0.000	0.000
110	A	112	ALA	0	-0.075	-0.042	30.969	0.055	0.055	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.056	-0.038	29.868	0.082	0.082	0.000	0.000	0.000	0.000
112	A	114	GLY	0	0.014	0.009	26.369	-0.215	-0.215	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.823	-0.909	20.223	-13.744	-13.744	0.000	0.000	0.000	0.000
114	A	116	ARG	1	0.812	0.937	24.362	9.445	9.445	0.000	0.000	0.000	0.000
115	A	117	LEU	0	0.056	0.031	23.061	-0.176	-0.176	0.000	0.000	0.000	0.000
116	A	118	SER	0	-0.038	-0.059	26.461	0.412	0.412	0.000	0.000	0.000	0.000
117	A	119	ASP	-1	-0.833	-0.936	28.948	-8.683	-8.683	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.913	-0.921	28.837	-9.634	-9.634	0.000	0.000	0.000	0.000
119	A	121	ASP	-1	-0.811	-0.897	24.855	-11.315	-11.315	0.000	0.000	0.000	0.000
120	A	122	VAL	0	-0.051	-0.023	26.860	-0.135	-0.135	0.000	0.000	0.000	0.000
121	A	123	ASP	-1	-0.871	-0.928	29.223	-8.579	-8.579	0.000	0.000	0.000	0.000
122	A	124	GLU	-1	-0.881	-0.930	26.198	-10.238	-10.238	0.000	0.000	0.000	0.000
123	A	125	ILE	0	0.016	0.014	23.381	-0.014	-0.014	0.000	0.000	0.000	0.000
124	A	126	ILE	0	-0.002	0.019	26.714	0.013	0.013	0.000	0.000	0.000	0.000
125	A	127	LYS	1	0.814	0.897	29.967	9.534	9.534	0.000	0.000	0.000	0.000
126	A	128	LEU	0	-0.029	-0.019	24.085	0.099	0.099	0.000	0.000	0.000	0.000
127	A	129	THR	0	-0.038	-0.031	25.674	-0.043	-0.043	0.000	0.000	0.000	0.000
128	A	130	ASP	-1	-0.899	-0.943	28.156	-8.471	-8.471	0.000	0.000	0.000	0.000
129	A	131	LEU	0	-0.061	-0.014	30.881	0.145	0.145	0.000	0.000	0.000	0.000
130	A	132	GLN	0	-0.077	-0.051	32.798	0.332	0.332	0.000	0.000	0.000	0.000
131	A	133	GLU	-1	-0.916	-0.967	36.622	-7.722	-7.722	0.000	0.000	0.000	0.000
132	A	134	ASP	-1	-0.842	-0.924	39.110	-7.153	-7.153	0.000	0.000	0.000	0.000
133	A	135	LEU	0	-0.059	-0.039	42.137	0.060	0.060	0.000	0.000	0.000	0.000
134	A	136	GLU	-1	-0.990	-0.998	44.869	-6.475	-6.475	0.000	0.000	0.000	0.000
135	A	137	GLY	0	-0.005	0.020	42.032	0.010	0.010	0.000	0.000	0.000	0.000
136	A	138	ASN	0	-0.116	-0.063	39.290	-0.226	-0.226	0.000	0.000	0.000	0.000
137	A	139	VAL	0	0.064	0.035	34.007	0.000	0.000	0.000	0.000	0.000	0.000
138	A	140	LYS	1	0.856	0.943	34.417	7.974	7.974	0.000	0.000	0.000	0.000
139	A	141	TYR	0	-0.012	-0.034	31.270	-0.304	-0.304	0.000	0.000	0.000	0.000
140	A	142	GLU	-1	-0.852	-0.940	29.877	-9.888	-9.888	0.000	0.000	0.000	0.000
141	A	143	ASP	-1	-0.896	-0.958	28.955	-9.535	-9.535	0.000	0.000	0.000	0.000
142	A	144	PHE	0	0.006	0.009	27.179	-0.258	-0.258	0.000	0.000	0.000	0.000
143	A	145	VAL	0	0.014	0.005	24.600	-0.385	-0.385	0.000	0.000	0.000	0.000
144	A	146	LYS	1	0.836	0.909	24.271	9.522	9.522	0.000	0.000	0.000	0.000
145	A	147	LYS	1	0.871	0.930	24.188	9.232	9.232	0.000	0.000	0.000	0.000
146	A	148	VAL	0	-0.003	0.002	21.632	-0.298	-0.298	0.000	0.000	0.000	0.000
147	A	149	MET	0	-0.085	-0.044	19.686	-0.300	-0.300	0.000	0.000	0.000	0.000
148	A	150	ALA	0	-0.025	0.011	19.357	-0.600	-0.600	0.000	0.000	0.000	0.000
149	A	151	GLY	0	0.041	0.033	19.357	-0.553	-0.553	0.000	0.000	0.000	0.000
150	A	152	PRO	0	-0.047	-0.035	18.861	0.475	0.475	0.000	0.000	0.000	0.000
151	A	153	TYR	0	-0.080	-0.078	18.872	0.735	0.735	0.000	0.000	0.000	0.000
152	A	154	PRO	-1	-0.930	-0.918	19.670	-13.551	-13.551	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)